.TH g_current 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_current - calculate current autocorrelation function of system

.B VERSION 4.5
.SH SYNOPSIS
\f3g_current\fP
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-f" " traj.xtc "
.BI "\-o" " current.xvg "
.BI "\-caf" " caf.xvg "
.BI "\-dsp" " dsp.xvg "
.BI "\-md" " md.xvg "
.BI "\-mj" " mj.xvg "
.BI "\-mc" " mc.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-sh" " int "
.BI "\-[no]nojump" ""
.BI "\-eps" " real "
.BI "\-bfit" " real "
.BI "\-efit" " real "
.BI "\-bvit" " real "
.BI "\-evit" " real "
.BI "\-tr" " real "
.BI "\-temp" " real "
.SH DESCRIPTION
\&This is a tool for calculating the current autocorrelation function, the correlation
\&of the rotational and translational dipole moment of the system, and the resulting static
\&dielectric constant. To obtain a reasonable result the index group has to be neutral.
\&Furthermore the routine is capable of extracting the static conductivity from the current 
\&autocorrelation function, if velocities are given. Additionally an Einstein\-Helfand fit also
\&allows to get the static conductivity.


\&The flag \fB \-caf\fR is for the output of the current autocorrelation function and \fB \-mc\fR writes the
\&correlation of the rotational and translational part of the dipole moment in the corresponding
\&file. However this option is only available for trajectories containing velocities.
\&Options \fB \-sh\fR and \fB \-tr\fR are responsible for the averaging and integration of the
\&autocorrelation functions. Since averaging proceeds by shifting the starting point
\&through the trajectory, the shift can be modified with \fB \-sh\fR to enable the choice of uncorrelated
\&starting points. Towards the end, statistical inaccuracy grows and integrating the
\&correlation function only yields reliable values until a certain point, depending on
\&the number of frames. The option \fB \-tr\fR controls the region of the integral taken into account
\&for calculating the static dielectric constant.
\&


\&Option \fB \-temp\fR sets the temperature required for the computation of the static dielectric constant.
\&


\&Option \fB \-eps\fR controls the dielectric constant of the surrounding medium for simulations using
\&a Reaction Field or dipole corrections of the Ewald summation (eps=0 corresponds to
\&tin\-foil boundary conditions).
\&


\&\fB \-[no]nojump\fR unfolds the coordinates to allow free diffusion. This is required to get a continuous
\&translational dipole moment, required for the Einstein\-Helfand fit. The resuls from the fit allow to
\&determine the dielectric constant for system of charged molecules. However it is also possible to extract
\&the dielectric constant from the fluctuations of the total dipole moment in folded coordinates. But this
\&options has to be used with care, since only very short time spans fulfill the approximation, that the density
\&of the molecules is approximately constant and the averages are already converged. To be on the safe side,
\&the dielectric constant should be calculated with the help of the Einstein\-Helfand method for
\&the translational part of the dielectric constant.
.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-o" " current.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-caf" " caf.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-dsp" " dsp.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-md" " md.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-mj" " mj.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-mc" " mc.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-sh"  " int" " 1000" 
 Shift of the frames for averaging the correlation functions and the mean\-square displacement.

.BI "\-[no]nojump"  "yes   "
 Removes jumps of atoms across the box.

.BI "\-eps"  " real" " 0     " 
 Dielectric constant of the surrounding medium. eps=0.0 corresponds to eps=infinity (thinfoil boundary conditions).

.BI "\-bfit"  " real" " 100   " 
 Begin of the fit of the straight line to the MSD of the translational fraction of the dipole moment.

.BI "\-efit"  " real" " 400   " 
 End of the fit of the straight line to the MSD of the translational fraction of the dipole moment.

.BI "\-bvit"  " real" " 0.5   " 
 Begin of the fit of the current autocorrelation function to a*tb.

.BI "\-evit"  " real" " 5     " 
 End of the fit of the current autocorrelation function to a*tb.

.BI "\-tr"  " real" " 0.25  " 
 Fraction of the trajectory taken into account for the integral.

.BI "\-temp"  " real" " 300   " 
 Temperature for calculating epsilon.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
